MIRACUM-Pipe: An Adaptable Pipeline for Next-Generation Sequencing Analysis, Reporting, and Visualization for Clinical Decision Making

Metzger P, Hess ME, Blaumeiser A, Pauli T, Schipperges V, Mertes R, Christoph J, Unberath P, Reimer N, Scheible R, Illert AL, Busch H, Andrieux G, Boerries M (2023)

Publication Type: Journal article

Publication year: 2023

Journal

Cancers MDPI

Book Volume: 15

Article Number: 3456

Journal Issue: 13

DOI: 10.3390/cancers15133456

Abstract

(1) Background: Next-generation sequencing (NGS) of patients with advanced tumors is becoming an established method in Molecular Tumor Boards. However, somatic variant detection, interpretation, and report generation, require in-depth knowledge of both bioinformatics and oncology. (2) Methods: MIRACUM-Pipe combines many individual tools into a seamless workflow for comprehensive analyses and annotation of NGS data including quality control, alignment, variant calling, copy number variation estimation, evaluation of complex biomarkers, and RNA fusion detection. (3) Results: MIRACUM-Pipe offers an easy-to-use, one-prompt standardized solution to analyze NGS data, including quality control, variant calling, copy number estimation, annotation, visualization, and report generation. (4) Conclusions: MIRACUM-Pipe, a versatile pipeline for NGS, can be customized according to bioinformatics and clinical needs and to support clinical decision-making with visual processing and interactive reporting.

Authors with CRIS profile

Philipp Unberath Lehrstuhl für Medizinische Informatik

Involved external institutions

Universitätsklinikum Freiburg DE Germany (DE) Martin-Luther-Universität Halle-Wittenberg (MLU) DE Germany (DE) Universität zu Lübeck DE Germany (DE) Klinikum rechts der Isar DE Germany (DE) Deutsches Krebsforschungszentrum (DKFZ) DE Germany (DE)

How to cite

APA:

Metzger, P., Hess, M.E., Blaumeiser, A., Pauli, T., Schipperges, V., Mertes, R.,... Boerries, M. (2023). MIRACUM-Pipe: An Adaptable Pipeline for Next-Generation Sequencing Analysis, Reporting, and Visualization for Clinical Decision Making. Cancers, 15(13). https://doi.org/10.3390/cancers15133456

MLA:

Metzger, Patrick, et al. "MIRACUM-Pipe: An Adaptable Pipeline for Next-Generation Sequencing Analysis, Reporting, and Visualization for Clinical Decision Making." Cancers 15.13 (2023).

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